From d17369e0ac543528328e792c8c8a22dbe3370718 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 21 Jun 2012 16:04:25 -0400 Subject: [PATCH] A few misc. residual errors in last commit --- .../sting/utils/codecs/hapmap/HapMapUnitTest.java | 5 +++-- .../sting/utils/codecs/vcf/IndexFactoryUnitTest.java | 4 ++-- .../utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java | 2 +- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java index 914783ca8..635779880 100644 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java @@ -27,6 +27,7 @@ package org.broadinstitute.sting.utils.codecs.hapmap; import org.broad.tribble.annotation.Strand; import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.PositionalBufferedStream; +import org.broadinstitute.sting.BaseTest; import org.testng.Assert; import org.testng.annotations.Test; @@ -38,9 +39,9 @@ import java.io.IOException; /** * Unit tests for the HapMap codec */ -public class HapMapUnitTest { +public class HapMapUnitTest extends BaseTest { // our sample hapmap file - private final static File hapMapFile = new File("public/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap"); + private final static File hapMapFile = new File(privateTestDir + "genotypes_chr1_ASW_phase3.3_first500.hapmap"); private final static String knownLine = "rs2185539 C/T chr1 556738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_r" + "s2185539:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC TC TT CT CC CC CC CC CC CC CC CC CC"; /** diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java index 6b16ffa0a..41ea587be 100755 --- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java @@ -27,8 +27,8 @@ import java.util.EnumSet; */ public class IndexFactoryUnitTest extends BaseTest { - File inputFile = new File("public/testdata/HiSeq.10000.vcf"); - File outputFile = new File("public/testdata/onTheFlyOutputTest.vcf"); + File inputFile = new File(privateTestDir + "HiSeq.10000.vcf"); + File outputFile = new File(privateTestDir + "onTheFlyOutputTest.vcf"); File outputFileIndex = Tribble.indexFile(outputFile); private SAMSequenceDictionary dict; diff --git a/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java index 82b17f70e..c05b11cf7 100644 --- a/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java @@ -25,7 +25,7 @@ import net.sf.samtools.SAMSequenceRecord; * Basic unit test for GenomeLoc */ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest { - private File simpleFasta = new File(privateTestDir + "/exampleFASTA.fasta"); + private File simpleFasta = new File(publicTestDir + "/exampleFASTA.fasta"); private static final int STEP_SIZE = 1; //private static final List QUERY_SIZES = Arrays.asList(1);